I have this same bug. It drives me nuts. It began with the 1.21 update, and it also resets the pirate mission counter. In other words, once the pirates complete a mission, and they tell me they have, I can send another mission right away. This eventually gets to the point that I can send a mission every three or four seconds when I should need to wait five minutes, even during a multiplayer game.
I only play multiplayer via direct connections. I'm curious if Flannicus uses ICO or not, that might be part of the issue.
I don't have a save or replay available (The bug drives me off the deep end in longer games. I don't even give them missions anymore unless I'm desperate and backed into a corner), but at least I know I'm not the only one who has this issue anymore.
